A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
Abstract Background The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-02-01
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| Series: | BMC Biology |
| Online Access: | https://doi.org/10.1186/s12915-020-0744-3 |
| _version_ | 1818610159651389440 |
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| author | Thomas Badet Ursula Oggenfuss Leen Abraham Bruce A. McDonald Daniel Croll |
| author_facet | Thomas Badet Ursula Oggenfuss Leen Abraham Bruce A. McDonald Daniel Croll |
| author_sort | Thomas Badet |
| collection | DOAJ |
| description | Abstract Background The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures. Results Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species. Conclusions Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions. |
| first_indexed | 2024-12-16T15:10:00Z |
| format | Article |
| id | doaj.art-8aadf1d8163b48f3928cce1726b21b9c |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-12-16T15:10:00Z |
| publishDate | 2020-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-8aadf1d8163b48f3928cce1726b21b9c2022-12-21T22:27:00ZengBMCBMC Biology1741-70072020-02-0118111810.1186/s12915-020-0744-3A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria triticiThomas Badet0Ursula Oggenfuss1Leen Abraham2Bruce A. McDonald3Daniel Croll4Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelLaboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelLaboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelPlant Pathology, Institute of Integrative Biology, ETH ZürichLaboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelAbstract Background The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures. Results Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species. Conclusions Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.https://doi.org/10.1186/s12915-020-0744-3 |
| spellingShingle | Thomas Badet Ursula Oggenfuss Leen Abraham Bruce A. McDonald Daniel Croll A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici BMC Biology |
| title | A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici |
| title_full | A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici |
| title_fullStr | A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici |
| title_full_unstemmed | A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici |
| title_short | A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici |
| title_sort | 19 isolate reference quality global pangenome for the fungal wheat pathogen zymoseptoria tritici |
| url | https://doi.org/10.1186/s12915-020-0744-3 |
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